LAMMPS (17 Feb 2022)
#===========================================================================#
# Rigid sphere freely moving near a stationary plane wall in a system       #
#   undergoing shear flow.                                                  #
# Every 10 time steps the center of mass velocity and angular velocity of   #
#   the sphere are printed to the screen.                                   #
# To run this example, LAMMPS needs to be compiled with a the following     #
# packages: RIGID, LATBOLTZ                                                 #
#                                                                           #
#===========================================================================#

units          micro
dimension      3
boundary       p p f
atom_style     atomic

#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
#   to ensure that the particles belonging to a given processor remain inside
#   that processors lattice-Boltzmann grid.
# The arguments for neigh_modify have been set to "delay 0 every 1", again
#   to ensure that the particles belonging to a given processor remain inside
#   that processors lattice-Boltzmann grid.  However, these values can likely
#   be somewhat increased without issue.  If a problem does arise (a particle
#   is outside of its processors LB grid) an error message is printed and
#   the simulation is terminated.
# The communcation cutoff is set to 2.5 dx to ensure that all particles in the
#   processor ghost fluid region (of width 2dx) are known to local processor.
#----------------------------------------------------------------------------
neighbor       1.0 bin
neigh_modify   delay 0 every 1
comm_modify cutoff 10.0

read_data      data.one_radius16d2
Reading data file ...
  orthogonal box = (-120 -120 -120) to (120 120 120)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  320 atoms
  read_data CPU = 0.015 seconds

#----------------------------------------------------------------------------
# None of the particles interact with one another.
#----------------------------------------------------------------------------
pair_style     lj/cut 2.45
pair_coeff     * * 0.0 0.0 2.45
neigh_modify   exclude type 1 1

mass           * 1.0

timestep       4.0

group          sphere1 id <> 1 320
320 atoms in group sphere1

#----------------------------------------------------------------------------
# Colloidal particle is initially stationary.
#----------------------------------------------------------------------------
velocity       all set 0.0 0.0 0.0 units box

#----------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# All of the particles in the simulation apply a force to the fluid.
#   (however, this fix does not explicitly apply a force back on to these
#    particles...this is accomplished through the use of the lb/viscous fix.
# Use a fluid density = 1.0, fluid viscosity = 1.0 (water), and a lattice
#   spacing dx=4.0.
# Use the trilinear interpolation stencil (default) to distribute the force
#   from a given particle onto the fluid mesh.
# Create shear in the system, by giving the upper z-wall a velocity of 0.0001
#   along the y-direction, while keeping the lower z-wall stationary.
#-----------------------------------------------------------------------------
fix   1 all lb/fluid 1 1.0 1.0 dx 4.0 zwall_velocity 0.0 0.0001
Using a lattice-Boltzmann grid of 60 by 60 by 61 total grid points. (../fix_lb_fluid.cpp:486)
Local Grid Geometry created. (../fix_lb_fluid.cpp:1018)

#----------------------------------------------------------------------------
# Apply the force due to the fluid onto the particles.
#----------------------------------------------------------------------------
fix   2 all lb/viscous

#----------------------------------------------------------------------------
# Integrate the motion of the particles, constraining them to move and
#   rotate together as a single rigid spherical object.  Use the first
#   version to allow the sphere to freely rotate and move with the fluid
#   and the 2nd version to measure the force and torque on a fixed sphere
#   in the shear flow which will allow you to measure the Stokes drag and
#   torque on the sphere.
#----------------------------------------------------------------------------
fix   3 all rigid group 1 sphere1
  1 rigid bodies with 320 atoms
#fix   3 all rigid group 1 sphere1 force * off off off torque * off off off

#----------------------------------------------------------------------------
# Create variables for the center-of-mass velocities, angular velocities, and
#   force and torque on the CM.  Then output these quantities to the screen.
#----------------------------------------------------------------------------
variable vx equal vcm(all,x)
variable vy equal vcm(all,y)
variable vz equal vcm(all,z)
variable omegax equal omega(all,x)
variable omegay equal omega(all,y)
variable omegaz equal omega(all,z)
variable fx equal fcm(all,x)
variable fy equal fcm(all,y)
variable fz equal fcm(all,z)
variable tx equal torque(all,x)
variable ty equal torque(all,y)
variable tz equal torque(all,z)

thermo_style   custom v_vx v_vy v_vz v_omegax v_omegay v_omegaz v_fx v_fy v_fz v_tx v_ty v_tz
thermo         100

run   7500

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- fix lb/fluid command:

@Article{Denniston et al.,
 author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,F.E. Mackay, S.T.T. Ollila, T. Whitehead},
 title =   {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid}, journal = {Comp.~Phys.~Comm.},
 year =    2022,
 volume =  275,
 pages =   {108318}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 3.45
  ghost atom cutoff = 10
  binsize = 1.725, bins = 140 140 140
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 8.426 | 8.426 | 8.426 Mbytes
v_vx v_vy v_vz v_omegax v_omegay v_omegaz v_fx v_fy v_fz v_tx v_ty v_tz 
           0            0            0            0            0            0            0            0            0            0            0            0 
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2.2614166e-13 3.5465948e-07 -9.9990351e-12 -1.2716738e-08 -5.1515303e-13 1.1802563e-12 4.4099503e-13 6.2398067e-07 -1.4010079e-11 -3.2779726e-06 -5.5610241e-11 3.8420418e-10 
9.9446526e-13 1.6203654e-06 -2.9965809e-11 -4.2770461e-08 -1.8551769e-12 3.935908e-12 7.0873308e-13 1.3654678e-06 -1.6036096e-11 -4.7351845e-06 -9.5164548e-11 5.5370816e-10 
1.8577304e-12 3.6408926e-06 -4.7867194e-11 -7.6340276e-08 -3.4227185e-12 7.0027746e-12 6.4525598e-13 1.8162442e-06 -1.2450308e-11 -4.49885e-06 -9.721214e-11 5.2404154e-10 
2.5784818e-12 6.0541618e-06 -6.1511675e-11 -1.0586215e-07 -4.8340636e-12 9.6842864e-12 5.0954806e-13 2.0115015e-06 -9.6836459e-12 -3.7358552e-06 -8.3756951e-11 4.3294805e-10 
3.1388911e-12 8.606157e-06 -7.2849939e-11 -1.2968814e-07 -5.9880947e-12  1.18341e-11 3.9602348e-13 2.0531243e-06 -8.7301633e-12  -2.9477e-06 -6.7497759e-11 3.3979481e-10 
3.5088487e-12 1.1153105e-05 -8.4778552e-11 -1.4827121e-07 -6.9042127e-12 1.3490413e-11 1.4926704e-13 2.012457e-06 -1.1121284e-11 -2.2774279e-06 -5.6689366e-11 2.5766138e-10 
3.6203369e-12 1.3620493e-05 -1.0074918e-10 -1.6255823e-07 -7.6327828e-12 1.4733197e-11 2.8190134e-14 1.9308502e-06 -1.3951766e-11 -1.743828e-06 -4.5410719e-11 1.9387811e-10 
3.5893239e-12 1.5972746e-05 -1.1992769e-10 -1.7347444e-07 -8.2060683e-12 1.5658564e-11 -7.5902354e-14 1.8309433e-06 -1.6655785e-11 -1.3300214e-06 -3.6956327e-11 1.4453207e-10 
3.4369216e-12 1.8195336e-05 -1.4242882e-10 -1.8179239e-07 -8.6609693e-12 1.6339062e-11 -1.5582523e-13 1.7248165e-06 -1.9125572e-11 -1.0126439e-06 -3.0479042e-11 1.0521684e-10 
3.1272907e-12 2.0284863e-05 -1.6693014e-10 -1.8812271e-07 -9.0539095e-12 1.6840547e-11 -3.2806998e-13 1.6187734e-06 -1.7338933e-11 -7.7034531e-07 -4.18956e-11 7.893297e-11 
2.6336268e-12 2.2243653e-05 -1.8945116e-10 -1.9293745e-07 -9.4581385e-12 1.720649e-11 -4.4473581e-13 1.5159979e-06 -1.8187251e-11 -5.858335e-07 -3.9427386e-11 5.7483932e-11 
2.0046303e-12 2.4076859e-05 -2.0991971e-10 -1.9659836e-07 -9.7540611e-12 1.7464607e-11 -5.3232938e-13 1.417998e-06 -1.33357e-11 -4.4535934e-07 -2.2183067e-11 4.087927e-11 
1.8043659e-12  2.57909e-05 -2.251392e-10 -1.9938137e-07 -9.9135163e-12 1.7702226e-11 -8.1829532e-14 1.3253893e-06 -1.1758285e-11 -3.3855787e-07 -1.1111144e-11 3.6790045e-11 
1.6716765e-12 2.7392642e-05 -2.3970723e-10 -2.0149677e-07 -1.0039419e-11 1.7837499e-11 -9.9475985e-14 1.2383189e-06 -1.1662512e-11 -2.5732441e-07 -9.4988118e-12 2.1805637e-11 
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1.4100591e-12 3.0286556e-05 -2.6363101e-10 -2.0432561e-07 -1.0375492e-11 1.7885827e-11 -2.116508e-13 1.0803004e-06 -7.2760242e-12 -1.484988e-07 -1.9669998e-11 -3.7541543e-12 
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-1.2278986e-12 3.3948917e-05 -2.7737567e-10 -2.0649056e-07 -1.0269686e-11 1.7690544e-11 -2.7606089e-13 8.7976413e-07 1.1137199e-12 -6.4828506e-08 5.969611e-12 6.1895863e-12 
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-3.5852249e-12 4.2445791e-05 -2.1618947e-10 -2.080656e-07 -9.4749377e-12 1.7845812e-11 1.0655839e-13 4.1407045e-07 5.2707815e-12 -2.6881271e-09 1.5541392e-11 -1.5116726e-12 
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-3.1820565e-12 4.3413174e-05 -2.0519131e-10 -2.0809376e-07 -9.2323294e-12 1.782123e-11 2.7307342e-13 3.6104485e-07 4.5405606e-12 -1.381731e-09 7.844705e-12 -2.1593177e-11 
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-6.8078423e-14 4.4637011e-05  -1.9017e-10 -2.0811091e-07 -9.2985302e-12 1.7560504e-11 2.3613824e-13 2.9396314e-07 2.8306791e-12 -3.6072498e-10 1.919591e-12 5.7324777e-14 
-2.6872645e-13 4.4992159e-05 -1.8489448e-10 -2.081129e-07 -9.1988109e-12 1.7585096e-11 -3.7386314e-13 2.7449607e-07 4.3641203e-12 -2.0179873e-10 1.7903185e-11 9.4883417e-12 
-7.6146932e-13 4.5323788e-05 -1.7973612e-10 -2.0811387e-07 -9.067395e-12 1.7625673e-11 -4.0029726e-13 2.5631874e-07 3.8153502e-12 -7.7154264e-11 1.864561e-11 7.0852862e-12 
-1.0073144e-12 4.5633459e-05 -1.7567167e-10 -2.0811405e-07 -8.9461618e-12 1.7602722e-11 -8.8146729e-14 2.3934617e-07 2.900483e-12 1.3609831e-11 1.8144897e-11 -1.0950951e-12 
-1.1183452e-12 4.5922622e-05 -1.7267861e-10 -2.0811371e-07 -8.8220108e-12 1.7567954e-11 -8.7131925e-14 2.2349647e-07 1.9871901e-12 7.3396979e-11 1.8201205e-11 -3.3808282e-12 
-1.2336249e-12 4.6192637e-05 -1.7082009e-10 -2.0811304e-07 -8.6931853e-12 1.7534253e-11 -1.0358975e-13 2.0869604e-07 9.8971584e-13 1.1034572e-10 1.8570854e-11 -4.1945968e-12 
-1.395039e-12 4.644477e-05 -1.7090836e-10 -2.0811204e-07 -8.5394724e-12 1.7470422e-11 -2.2192138e-13 1.9487513e-07 -1.0653437e-12 1.5048013e-10 2.2960595e-11 -7.9254026e-12 
-1.5887239e-12 4.6680205e-05 -1.726235e-10 -2.0811078e-07 -8.3735722e-12 1.7394789e-11 5.3191009e-14 1.8196634e-07 -1.4136613e-12 2.2963534e-10 2.654505e-11 -1.8261053e-12 
-1.4689452e-12 4.6900047e-05 -1.7480066e-10 -2.081091e-07 -8.2058094e-12 1.7351678e-11 1.2094829e-13 1.6991911e-07 -2.6013388e-12 2.4677201e-10  1.76692e-11 -7.1825235e-12 
-1.3595687e-12 4.7105333e-05 -1.7899795e-10 -2.081074e-07 -8.0435813e-12 1.7311436e-11 -2.3058185e-13 1.586669e-07 -5.9352116e-12 2.143538e-10 3.2425344e-11 -1.0330713e-11 
-1.6431943e-12 4.7297025e-05 -1.8929524e-10 -2.0810597e-07 -7.7996954e-12 1.7199148e-11 -2.3195078e-13 1.4815965e-07 -9.1089087e-12 2.0069043e-10 2.7268474e-11 -1.5424889e-11 
-1.9503819e-12 4.7476021e-05 -2.0221518e-10 -2.0810468e-07 -7.655314e-12 1.7080428e-11 -2.618849e-13 1.383469e-07 -1.0767028e-11 1.6168876e-10 1.2892606e-11 -1.6616695e-11 
-2.293052e-12 4.7643164e-05 -2.1485895e-10 -2.0810355e-07 -7.6010878e-12 1.6957401e-11 -2.8846319e-13 1.2918561e-07 -9.5229628e-12 1.583733e-10 4.7988904e-12 -1.7439504e-11 
-2.5677362e-12 4.7799238e-05 -2.3224794e-10 -2.0810274e-07 -7.733652e-12 1.6817843e-11 4.7024153e-15 1.2062891e-07 -1.6977112e-11 1.0067875e-10 -5.9706483e-12 -6.6309632e-12 
-2.5737947e-12 4.7944975e-05 -2.542538e-10 -2.0810213e-07 -7.6510888e-12 1.676216e-11 -3.154599e-14 1.1264034e-07 -1.7155189e-11 8.6731774e-11 1.320634e-11 -5.9239428e-12 
-3.3012431e-12 4.808106e-05 -2.7606974e-10 -2.0810154e-07 -7.5285751e-12 1.6730121e-11 -5.5195274e-13 1.051819e-07 -1.8102675e-11 7.9086408e-11 2.549833e-11 3.8248179e-12 
-4.0407963e-12 4.8208133e-05 -2.9913872e-10 -2.0810087e-07 -7.3675841e-12 1.6729661e-11 -1.056947e-13 9.8215693e-08 -2.0564122e-11 8.9889186e-11 9.0969559e-12 -5.0411456e-12 
-4.0017866e-12 4.8326792e-05 -3.2578824e-10 -2.0810019e-07 -7.3309734e-12 1.6685377e-11 3.9903591e-14 9.1714102e-08 -2.2544733e-11 9.4144708e-11 -9.2931714e-12 5.3254879e-12 
-3.7606866e-12 4.8437596e-05 -3.5569049e-10 -2.080996e-07 -7.4780802e-12 1.6680934e-11 2.7466593e-13 8.5641003e-08 -2.425075e-11 7.7669196e-11 -2.2631547e-11 5.8077979e-13 
-3.4574887e-12 4.8541063e-05 -3.8545474e-10 -2.0809901e-07 -7.6093713e-12 1.6646067e-11 2.5876746e-14 7.997313e-08 -2.317586e-11 1.0544046e-10 -1.5314944e-11 6.8357155e-12 
-2.9114149e-12 4.8637681e-05 -4.1425452e-10 -2.0809838e-07 -7.7070087e-12 1.6659672e-11 6.2786281e-13 7.4677646e-08 -2.2436087e-11 8.9235324e-11 -1.3645085e-11 1.4694507e-11 
-2.2825362e-12 4.8727902e-05 -4.4462584e-10 -2.0809808e-07 -7.7463431e-12 1.6727387e-11 4.986996e-13 6.973271e-08 -2.3823592e-11 4.8349103e-11 -4.917953e-12 1.0180248e-11 
-1.6721448e-12 4.881215e-05 -4.7395477e-10 -2.080978e-07 -7.798864e-12 1.6781065e-11 5.8461703e-13 6.5116697e-08 -2.2923269e-11 3.3917578e-11 -1.4512356e-11 3.0753823e-12 
-1.0108835e-12 4.889082e-05 -5.0054848e-10 -2.0809742e-07 -7.8734886e-12 1.6821117e-11 5.5262937e-13 6.0804995e-08 -2.0048603e-11 6.7540691e-11 -9.5748309e-12 5.1419531e-12 
-5.2913704e-13 4.8964281e-05 -5.2361079e-10 -2.0809688e-07 -7.9342525e-12 1.6809498e-11 1.7857863e-13 5.6779412e-08 -1.7008275e-11 8.4873628e-11 -8.0821684e-12 -1.3432203e-11 
-6.0869323e-13 4.9032877e-05 -5.4391464e-10 -2.0809612e-07 -7.9700834e-12 1.6669189e-11 -2.2181063e-13 5.3018043e-08 -1.6188875e-11 1.2254388e-10 -3.4719243e-12 -2.5582696e-11 
5.3160987e-14 4.909693e-05 -5.685844e-10 -2.0809534e-07 -7.8445232e-12 1.6543112e-11 3.7931128e-13 4.9508006e-08 -2.3478774e-11 1.0539577e-10 3.8278786e-11 -1.7435743e-11 
6.9879599e-13 4.9156741e-05 -6.0029127e-10 -2.0809434e-07 -7.4710339e-12 1.6485438e-11 5.2135936e-13 4.6228138e-08 -2.7953013e-11 1.1306415e-10 3.9827585e-11 -4.0676347e-12 
1.3291032e-12 4.921259e-05 -6.3478917e-10 -2.0809343e-07 -7.1919325e-12 1.6475734e-11 8.0744289e-13 4.3164468e-08 -2.9352787e-11 1.9393928e-10 2.1395748e-11 -1.3540015e-11 
1.9099631e-12 4.9264739e-05 -6.713946e-10 -2.0809198e-07 -7.14109e-12 1.6362552e-11 5.0399245e-13 4.0306735e-08 -3.0085714e-11 2.4238628e-10 -1.2562062e-11 -3.1127285e-11 
2.5888559e-12 4.9313435e-05 -7.0699965e-10 -2.0809031e-07 -7.149238e-12 1.6227991e-11 5.2667785e-13 3.7637786e-08 -2.8432993e-11 2.6235217e-10 -2.232043e-12 -2.2764185e-11 
3.2694582e-12 4.9358908e-05 -7.414765e-10 -2.0808825e-07 -7.1300019e-12 1.6100817e-11 5.4583215e-13 3.5147252e-08 -2.5050106e-11 3.5891383e-10 3.6724193e-12 -1.8864321e-11 
3.3319364e-12 4.9401369e-05 -7.717209e-10 -2.0808576e-07 -7.1044853e-12 1.6070581e-11 -1.2307553e-12 3.2817485e-08 -1.9476032e-11 3.1425065e-10 2.5407039e-13 2.4318892e-12 
1.3098859e-12 4.9441018e-05 -7.9443484e-10 -2.0808358e-07 -7.0912957e-12 1.6079833e-11 -1.9382883e-12 3.0644803e-08 -1.7818422e-11 3.1668434e-10 -1.5502234e-12 -3.3879027e-12 
-9.4132416e-13 4.9478041e-05 -8.1438431e-10 -2.0808148e-07 -7.0899773e-12 1.6074809e-11 -1.1537277e-12 2.8614527e-08 -1.2295571e-11 2.623115e-10 -1.1222739e-12 6.3245613e-12 
-1.6613373e-12 4.9512612e-05 -8.2794953e-10 -2.0807969e-07 -7.0886692e-12 1.6035491e-11 -3.2150631e-13 2.6719935e-08 -1.0632544e-11 2.5483461e-10 -7.889241e-13 -4.5931115e-12 
-2.0923849e-12 4.9544894e-05 -8.4103126e-10 -2.080779e-07 -7.0787296e-12 1.598084e-11 -3.6458701e-13 2.4950759e-08 -1.0668225e-11 2.5363261e-10 2.557409e-12 -7.4330019e-12 
-2.6074079e-12 4.9575038e-05 -8.5484831e-10 -2.0807608e-07 -7.0458889e-12 1.5917995e-11 -4.6370161e-13 2.3298683e-08 -1.1706817e-11 2.5798545e-10 6.4493257e-12 -9.0570787e-12 
-3.1912867e-12 4.9603187e-05 -8.7103016e-10 -2.0807419e-07 -6.9729658e-12 1.5869196e-11 -5.4662034e-13 2.1756065e-08 -1.4183469e-11 2.6950321e-10 1.2401403e-11 -9.1121813e-12 
-2.6896504e-12 4.9629471e-05 -8.8354072e-10 -2.0807269e-07 -6.9518789e-12 1.5862597e-11 7.7697632e-13 2.0315473e-08 -9.1356461e-12 1.9455164e-10 -5.2929772e-13 -4.0871645e-12 
Loop time of 348.592 on 4 procs for 7500 steps with 320 atoms

Performance: 7435633235.428 ns/day, 0.000 hours/ns, 21.515 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.024506   | 0.025477   | 0.026424   |   0.6 |  0.01
Neigh   | 0.030494   | 0.03257    | 0.034614   |   1.0 |  0.01
Comm    | 0.2132     | 0.21532    | 0.22048    |   0.6 |  0.06
Output  | 0.011234   | 0.016341   | 0.031613   |   6.9 |  0.00
Modify  | 347.96     | 347.98     | 348        |   0.1 | 99.83
Other   |            | 0.3181     |            |       |  0.09

Nlocal:             80 ave          86 max          74 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost:         122.75 ave         126 max         120 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs:              0 ave           0 max           0 min
Histogram: 4 0 0 0 0 0 0 0 0 0

Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:05:48
